Phase II: Using Our Toolbox

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.title[
# Phase II: Using Our Toolbox
]
.subtitle[
## Module 7: Birds of a Feather
]
.author[
### Dr. Christopher Kenaley
]
.institute[
### Boston College
]
.date[
### 2024/14/11
]

---

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# In class today

```
## Warning: package 'ggplot2' was built under R version 4.2.3
```

<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.14.0/css/all.min.css">

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Today we'll ....

- Explore the logistic curve

![](https://resources.tidal.com/images/585b7fda/ecf7/4b71/b24d/ac41523e5bb2/1280x720.jpg)
]

.pull-right[

]

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## Module 8: Birds of a feather

![](https://www.allaboutbirds.org/guide/assets/photo/302314881-1280px.jpg)

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## Module 8: Birds of a feather

``` r
yr <- c(2021,2022,2023)

bhv_l <- list()

for(i in yr){
 bhv_l[[i]] <- occ_data(scientificName = "Vireo solitarius",
                year=i,
                month="3,6",
                limit=1000,
                country="US",
                basisOfRecord = "HUMAN_OBSERVATION",
                stateProvince="Massachusetts")[[2]] %>% 
   select(individualCount,
          year,month,day,
          decimalLongitude,
          decimalLatitude)
}

bhv <- do.call(rbind, bhv_l)
```

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## Module 8: Birds of a feather

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``` r
mass <- ne_states(country = 
                    "United States of America",
                  returnclass = "sf") %>% 
  filter(name=="Massachusetts") 
```
]

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``` r
mass %>% 
  ggplot() +
  geom_sf()+
  geom_point(data=bhv,
             aes(decimalLongitude,
                 decimalLatitude,
                 col=year))
```

![](3140_f24_11-11_files/figure-html/unnamed-chunk-4-1.png)
]

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## Module 8: Birds of a feather

.pull-left[

### The logistic curve
  
![](https://www.billharlan.com/papers/logistic/fig1.png)
]

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## Module 8: Birds of a feather

.pull-left[

### The logistic curve

``` r
bhv_arrive <- bhv%>%mutate(n=1:n()) %>%
  group_by(n) %>%
  mutate(date=as.Date(paste0(year,"-",month,"-",day)),
         j.day=julian(date,
                      origin=as.Date(paste0(unique(year),"-01-01")))
         )%>%
  na.omit() %>%
  group_by(year,j.day,date)%>%
  reframe(day.tot=sum(individualCount,na.rm=T))%>%
  group_by(year)%>%
  mutate(prop=cumsum(day.tot/sum(day.tot,na.rm = T)))
```
]

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``` r
bhv_arrive %>% 
  ggplot(aes(j.day,prop,col=as.factor(year))) +
  geom_point()
```

![](3140_f24_11-11_files/figure-html/unnamed-chunk-6-1.png)

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## Module 8: Birds of a feather

.pull-left[

### The logistic curve

``` r
bhv_pred <- bhv_arrive%>%
  group_by(year)%>%
 reframe(
   pred=predict(nls(prop~SSlogis(j.day,Asym, xmid, scal)),newdata=data.frame(j.day=min(j.day):max(j.day))),
   j.day=min(j.day):max(j.day),
  )%>%
  left_join(bhv_arrive%>%dplyr::select(j.day,date,prop)) 
```
]

.pull-right[

non-linear least squares using `nls` package

`SSlogis`:

- vector `input` *
- asymptote `Asym`*
- inflection point `xmid` *
- scale `scale` *

``` r
SSlogis(input,Asym, xmid, scal)
```
 
 * functions that compute these values
 ]
 
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## Module 8: Birds of a feather

.pull-left[

### The logistic curve

``` r
p <- bhv_pred %>% 
  ggplot(aes(j.day,prop),alpha=0.3) +
  geom_point()+
  geom_line(aes(j.day,pred,group=year),col="blue")
```
]

.pull-left[

```
## Warning: Removed 4 rows containing missing values or values outside the scale range
## (`geom_point()`).
```

![](3140_f24_11-11_files/figure-html/unnamed-chunk-10-1.png)
]